BN1144 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 1.6234e-06 6.2785e-06
Layer 3 2.7554e-06 3.7643e-04
Layer 2 2.1123e-05 2.2623e-02
Layer 5 5.4663e-05 5.3885e-04
Layer 6 1.5118e-03 1.0142e-02
WM 5.0234e-01 4.8557e-01
Layer 1 8.8414e-01 8.0503e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
MAGED1 Expression Distribution
Gene Specificity Score (GSS)
MAGED1 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
MAGED1 Layer 4 2.9531 0.8107
FBXW7 Layer 4 2.6777 0.8060
NUAK1 Layer 4 2.9219 0.8059
SPRYD3 Layer 4 2.5781 0.8027
MAPK8IP2 Layer 4 2.6484 0.7934
CLTA Layer 4 2.6309 0.7932
SEZ6L2 Layer 4 2.5332 0.7892
SORL1 Layer 4 2.5723 0.7889
ATP13A2 Layer 3 2.7754 0.7885
DYNLL2 Layer 4 2.6602 0.7885
COX7A2L Layer 5 2.5176 0.7884
MEF2C Layer 4 2.8281 0.7867
SLC12A5 Layer 5 2.5605 0.7843
INPP5F Layer 4 2.6484 0.7836
EIF5 Layer 4 2.7480 0.7831
MRPS21 Layer 4 2.7422 0.7813
EFR3A Layer 4 2.6836 0.7811
SLC6A17 Layer 5 2.6660 0.7789
ATXN7L3B Layer 4 3.1797 0.7775
CTBP1 Layer 4 2.6250 0.7766
ELAVL4 Layer 4 2.9531 0.7756
ABHD8 Layer 4 2.9160 0.7754
DMTN Layer 4 2.8086 0.7748
FKBP8 Layer 5 2.3750 0.7741
CPLX1 Layer 3 2.6836 0.7737
RNPS1 Layer 4 2.4512 0.7735
TUBB4B Layer 4 2.7852 0.7730
RUNDC3A Layer 3 2.6631 0.7718
SNCA Layer 5 2.4512 0.7712
SULT4A1 Layer 4 2.7070 0.7711
WBP2 Layer 4 2.3398 0.7708
SNX10 Layer 3 2.7070 0.7707
CHGA Layer 4 2.9922 0.7686
TCEA2 Layer 5 2.3965 0.7686
KLHDC3 Layer 4 2.9473 0.7681
PTPA Layer 4 2.8770 0.7671
OAT Layer 4 2.6426 0.7666
FLOT1 Layer 5 2.6016 0.7660
TUBB3 Layer 5 2.9277 0.7660
PRRT1 Layer 5 2.7012 0.7655
TMEM151B Layer 3 2.5215 0.7654
NRXN1 Layer 4 2.8965 0.7650
ATP5PO Layer 4 2.3926 0.7639
PCBP2 Layer 5 2.2930 0.7638
VDAC3 Layer 4 2.8027 0.7634
INA Layer 4 2.8516 0.7632
IQSEC1 Layer 5 2.9414 0.7630
MYCBP2 Layer 4 2.7012 0.7624
KLC2 Layer 4 2.7070 0.7619
ATP6V0A1 Layer 5 2.5215 0.7616

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1144
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1144_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1144/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1144/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1144/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1144/report/PD/BN1144_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1144/report/PD/BN1144_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 02:27:56
  • Number of Processes: 10
  • Spending Time: 0h 2m